Multitasking the "arduino" functionality

I noticed something odd this evening. It doesn't look like the "arduino" functionality of the PCD8 can multitask?

Basically - I added a "heartbeat" binary to my PCD so that I can, at a glance, see whether it's responding. This is the same basic functionality as is on my beaglebone and odroid. The binary is set to load on each reboot automatically via a cron job:

#include <core.h>
int led_pin = 13;
void setup() {
pinMode(led_pin, OUTPUT);
}
void loop() {
digitalWrite(led_pin, HIGH); // set the LED on
delay(100); // wait for a second
digitalWrite(led_pin, LOW); // set the LED off
delay(400); // wait for a second
digitalWrite(led_pin, HIGH); // set the LED on
delay(100); // wait for a second
digitalWrite(led_pin, LOW); // set the LED off
delay(1000); // wait for a second
}

The heartbeat blinker works fine. However, when I try to do something else, like blink an LED attached to each of the digital pins, one after the other, the output is interrupted by each "blink" of the blink binary...?